Variant report

Variant	rs16942796
Chromosome Location	chr15:45694137-45694138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:205)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:205 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45693792-45695227	GM12878	blood:	n/a	n/a
2	CEBPB	chr15:45694050-45695135	IMR90	lung:	n/a	n/a
3	POLR2A	chr15:45693983-45695356	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:45694025-45694878	PFSK-1	brain:	n/a	n/a
5	MAX	chr15:45693878-45695301	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:45694009-45695355	GM18526	blood:	n/a	n/a
7	POLR2A	chr15:45693992-45694956	HUVEC	blood vessel:	n/a	n/a
8	MAZ	chr15:45693871-45695868	K562	blood:	n/a	n/a
9	TEAD4	chr15:45693921-45694804	K562	blood:	n/a	n/a
10	POLR2A	chr15:45693764-45695111	K562	blood:	n/a	n/a
11	GTF2F1	chr15:45693910-45694725	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:45694069-45694880	HCT-116	colon:	n/a	n/a
13	POLR2A	chr15:45693891-45695837	HepG2	liver:	n/a	n/a
14	NFYA	chr15:45694023-45694757	Hela-S3	cervix:	n/a	chr15:45694463-45694481
15	MAX	chr15:45693960-45696081	Hela-S3	cervix:	n/a	n/a
16	MTA3	chr15:45693666-45695134	GM12878	blood:	n/a	n/a
17	TRIM28	chr15:45694063-45694776	K562	blood:	n/a	n/a
18	MBD4	chr15:45693958-45694690	HepG2	liver:	n/a	n/a
19	RCOR1	chr15:45693605-45695236	IMR90	lung:	n/a	n/a
20	USF2	chr15:45693976-45694705	Hela-S3	cervix:	n/a	chr15:45694130-45694141
21	MAX	chr15:45693906-45695241	GM12878	blood:	n/a	n/a
22	RCOR1	chr15:45693888-45696299	Hela-S3	cervix:	n/a	n/a
23	UBTF	chr15:45694004-45696027	K562	blood:	n/a	n/a
24	ZNF143	chr15:45694007-45695123	GM12878	blood:	n/a	n/a
25	TAF1	chr15:45694059-45695132	Hela-S3	cervix:	n/a	n/a
26	RELA	chr15:45693906-45694805	GM10847	blood:	n/a	n/a
27	POLR2A	chr15:45694081-45694828	HCT-116	colon:	n/a	n/a
28	TBL1XR1	chr15:45694028-45694613	K562	blood:	n/a	n/a
29	MAX	chr15:45693982-45694830	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr15:45694076-45696112	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr15:45693954-45695030	A549	lung:	n/a	n/a
32	HCFC1	chr15:45693468-45696451	Hela-S3	cervix:	n/a	n/a
33	TAF1	chr15:45694126-45694839	K562	blood:	n/a	n/a
34	POLR2A	chr15:45693853-45695894	Raji	blood:	n/a	n/a
35	STAT5A	chr15:45693692-45695160	GM12878	blood:	n/a	chr15:45693747-45693759
36	ZMIZ1	chr15:45694127-45694869	K562	blood:	n/a	n/a
37	NFATC1	chr15:45694115-45694722	GM12878	blood:	n/a	n/a
38	POLR2A	chr15:45694058-45694848	U87	brain:	n/a	n/a
39	PML	chr15:45694011-45694871	K562	blood:	n/a	n/a
40	POLR2A	chr15:45693786-45695803	GM19099	blood:	n/a	n/a
41	POLR2A	chr15:45694103-45694775	SK-N-MC	brain:	n/a	n/a
42	EP300	chr15:45694054-45694694	HepG2	liver:	n/a	n/a
43	SPI1	chr15:45694052-45694946	GM12878	blood:	n/a	chr15:45694559-45694572
44	MAX	chr15:45693952-45695215	K562	blood:	n/a	n/a
45	POLR2A	chr15:45693986-45695826	GM19193	blood:	n/a	n/a
46	ZNF143	chr15:45693970-45695039	H1-hESC	embryonic stem cell:	n/a	n/a
47	ELK1	chr15:45693918-45694830	Hela-S3	cervix:	n/a	n/a
48	CUX1	chr15:45693921-45694688	GM12878	blood:	n/a	n/a
49	PBX3	chr15:45694098-45694838	SK-N-SH	brain:	n/a	n/a
50	RELA	chr15:45693928-45694905	GM15510	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45471561..45475350-chr15:45693833..45697444,3	MCF-7	breast:
2	chr12:44199711..44200638-chr15:45694089..45695040,2	NB4	blood:
3	chr15:45443245..45445612-chr15:45693741..45696247,2	K562	blood:
4	chr11:67112594..67114538-chr15:45691318..45694198,2	MCF-7	breast:
5	chr15:45685120..45688238-chr15:45691728..45694195,3	MCF-7	breast:
6	chr15:45491292..45493253-chr15:45693461..45696308,4	K562	blood:
7	chr15:45459071..45462844-chr15:45693635..45696532,4	K562	blood:
8	chr15:45693902..45696245-chr15:45709725..45712520,2	K562	blood:
9	chr15:45570708..45573284-chr15:45693152..45695793,2	MCF-7	breast:
10	chr15:45693976..45694707-chrX:48957687..48958360,2	HCT-116	colon:
11	chr15:45694071..45694958-chr7:104653061..104653666,2	Hela-S3	cervix:
12	chr15:45458882..45460694-chr15:45692968..45695992,3	MCF-7	breast:
13	chr15:45692773..45694505-chr15:45738421..45740123,2	MCF-7	breast:
14	chr15:45694132..45694822-chr5:68665207..68665996,2	HCT-116	colon:
15	chr15:45693513..45696404-chr15:45876472..45881031,4	MCF-7	breast:
16	chr15:45489573..45492565-chr15:45693942..45696435,3	MCF-7	breast:
17	chr15:45693986..45696362-chr15:45736299..45740535,4	MCF-7	breast:
18	chr15:45490733..45493253-chr15:45692978..45696308,3	K562	blood:
19	chr15:45693917..45694984-chr6:160210614..160211334,3	Hela-S3	cervix:
20	chr15:45459427..45462384-chr15:45693635..45696116,3	K562	blood:
21	chr15:45693029..45695760-chr15:45741637..45746369,4	MCF-7	breast:
22	chr15:45693949..45694449-chr9:33290338..33290839,2	NB4	blood:
23	chr10:74033457..74033981-chr15:45693872..45694794,2	NB4	blood:
24	chr15:45693316..45695933-chr15:45878534..45881095,2	MCF-7	breast:
25	chr1:28975072..28975687-chr15:45694096..45694823,2	HCT-116	colon:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC30A4-1	chr15:45693879-45694520	ENSG00000230288
2	lnc-SLC30A4-1	chr15:45694097-45694525	ENSG00000230288.4
3	lnc-SLC30A4-1	chr15:45694097-45694513	NONHSAT042242

No data

Variant related genes	Relation type
SPATA5L1	TF binding region
GATM	TF binding region
ENSG00000086102	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000120438	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000137857	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000259354	Chromatin interaction
ENSG00000252285	Chromatin interaction
ENSG00000259520	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000151239	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000196998	Chromatin interaction
ENSG00000112110	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000260170	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1145073	0.85[GIH][hapmap]
rs1153851	0.85[GIH][hapmap]
rs1288847	0.91[GIH][hapmap]
rs16941118	1.00[GIH][hapmap]
rs16941127	1.00[GIH][hapmap]
rs16941245	1.00[GIH][hapmap]
rs1719249	1.00[GIH][hapmap]
rs2433605	0.85[GIH][hapmap]
rs2467857	0.85[GIH][hapmap]
rs2467873	0.91[GIH][hapmap]
rs2486289	0.85[GIH][hapmap]
rs60639238	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7175618	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9672959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9972443	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45693200-45694200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:45693200-45694200	Flanking Active TSS	Liver	Liver
3	chr15:45693200-45694200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr15:45693200-45694400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr15:45693200-45695000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:45693200-45696000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:45693200-45696400	Active TSS	Aorta	Aorta
8	chr15:45693200-45696800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:45693400-45694200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:45693400-45694200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr15:45693400-45694400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr15:45693400-45694600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:45693400-45695600	Active TSS	Brain Anterior Caudate	brain
14	chr15:45693400-45696000	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr15:45693400-45696000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr15:45693400-45696200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr15:45693400-45696600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr15:45693400-45697000	Active TSS	Fetal Intestine Large	intestine
19	chr15:45693400-45697600	Active TSS	GM12878-XiMat	blood
20	chr15:45693600-45694200	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr15:45693600-45694200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr15:45693600-45694200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr15:45693600-45694200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:45693600-45694200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr15:45693600-45694200	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr15:45693600-45694200	Active TSS	Right Atrium	heart
27	chr15:45693600-45694200	Flanking Active TSS	Thymus	Thymus
28	chr15:45693600-45694200	Flanking Active TSS	Hela-S3	cervix
29	chr15:45693600-45694200	Flanking Active TSS	HUVEC	blood vessel
30	chr15:45693600-45694400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr15:45693600-45694400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:45693600-45694400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr15:45693600-45694400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr15:45693600-45694600	Active TSS	Brain Germinal Matrix	brain
35	chr15:45693600-45694800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr15:45693600-45694800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:45693600-45694800	Active TSS	Colonic Mucosa	Colon
38	chr15:45693600-45695400	Active TSS	Right Ventricle	heart
39	chr15:45693600-45695600	Active TSS	Fetal Thymus	thymus
40	chr15:45693600-45695800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:45693600-45695800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:45693600-45695800	Active TSS	Fetal Brain Male	brain
43	chr15:45693600-45695800	Active TSS	K562	blood
44	chr15:45693600-45696000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr15:45693600-45696000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:45693600-45696000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr15:45693600-45696000	Active TSS	Fetal Intestine Small	intestine
48	chr15:45693600-45696000	Active TSS	Fetal Stomach	stomach
49	chr15:45693600-45696200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:45693600-45696200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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